chr10-1233837-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_018702.4(ADARB2):c.1370G>A(p.Arg457His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000527 in 1,613,624 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R457C) has been classified as Uncertain significance.
Frequency
Consequence
NM_018702.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADARB2 | NM_018702.4 | c.1370G>A | p.Arg457His | missense_variant | 6/10 | ENST00000381312.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADARB2 | ENST00000381312.6 | c.1370G>A | p.Arg457His | missense_variant | 6/10 | 1 | NM_018702.4 | P1 | |
LINC00200 | ENST00000655745.1 | n.265-54636C>T | intron_variant, non_coding_transcript_variant | ||||||
ADARB2 | ENST00000469464.1 | n.154G>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000671 AC: 102AN: 152116Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000590 AC: 148AN: 250722Hom.: 0 AF XY: 0.000516 AC XY: 70AN XY: 135540
GnomAD4 exome AF: 0.000512 AC: 748AN: 1461390Hom.: 3 Cov.: 33 AF XY: 0.000523 AC XY: 380AN XY: 726986
GnomAD4 genome ? AF: 0.000670 AC: 102AN: 152234Hom.: 0 Cov.: 31 AF XY: 0.000591 AC XY: 44AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.1370G>A (p.R457H) alteration is located in exon 6 (coding exon 6) of the ADARB2 gene. This alteration results from a G to A substitution at nucleotide position 1370, causing the arginine (R) at amino acid position 457 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at